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P38203 (LSM2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 124. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
U6 snRNA-associated Sm-like protein LSm2
Alternative name(s):
Small nuclear ribonucleoprotein D homolog SNP3
Gene names
Name:LSM2
Synonyms:SMX5, SNP3
Ordered Locus Names:YBL026W
ORF Names:YBL0425
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length95 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. Ref.7 Ref.8 Ref.9 Ref.11 Ref.12 Ref.14 Ref.15 Ref.16

Subunit structure

Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a doughnut shape. The LSm subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Except for LSM1, where a C-terminal helix crosses the ring structure to form additional interactions with LSM3 and LSM6, each subunit interacts only with its two neighboring subunits. The LSM1-LSM7 complex interacts with PAT1; within the complex PAT1 has direct interactions with LSM2 and LSM3. Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a doughnut shape; an RNA strand can pass through the hole in the center of the ring structure. The LSm subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. A complex comprising LSM2-LSM7 without LSM1 or LSM8 may exist. Likewise, LSM2 and LSM3 can assemble into a doughnut structure that binds PAT1 (in vitro). Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1. Ref.4 Ref.6 Ref.7 Ref.13 Ref.14 Ref.15 Ref.16

Subcellular location

Nucleus. Cytoplasm Probable.

Miscellaneous

Present with 2210 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the snRNP Sm proteins family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 9595U6 snRNA-associated Sm-like protein LSm2
PRO_0000125559

Experimental info

Mutagenesis351F → A: Strongly reduces affinity for poly-U RNA ends. Ref.16
Mutagenesis371N → A: Strongly reduces affinity for poly-U RNA ends. Ref.16
Mutagenesis631R → A: Strongly reduces affinity for poly-U RNA ends. Ref.14 Ref.16

Secondary structure

....................... 95
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P38203 [UniParc].

Last modified October 1, 1994. Version 1.
Checksum: C23856268CEE92E2

FASTA9511,163
        10         20         30         40         50         60 
MLFFSFFKTL VDQEVVVELK NDIEIKGTLQ SVDQFLNLKL DNISCTDEKK YPHLGSVRNI 

        70         80         90 
FIRGSTVRYV YLNKNMVDTN LLQDATRREV MTERK 

« Hide

References

« Hide 'large scale' references
[1]"Analysis of a 17.4 kb DNA segment of yeast chromosome II encompassing the ribosomal protein L19 as well as proteins with homologies to components of the hnRNP and snRNP complexes and to the human proliferation-associated p120 antigen."
van Dyck L., Jonniaux J.-L., Barreiros T.D.M., Kleine K., Goffeau A.
Yeast 10:1663-1673(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]"Complete DNA sequence of yeast chromosome II."
Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. expand/collapse author list , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin."
Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.
EMBO J. 18:3451-3462(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION WITH PRE-P RNA.
[5]"Characterization of Sm-like proteins in yeast and their association with U6 snRNA."
Mayes A.E., Verdone L., Legrain P., Beggs J.D.
EMBO J. 18:4321-4331(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[6]"Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP."
Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R., Fabrizio P.
EMBO J. 18:4535-4548(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
[7]"A Sm-like protein complex that participates in mRNA degradation."
Bouveret E., Rigaut G., Shevchenko A., Wilm M., Seraphin B.
EMBO J. 19:1661-1671(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE LSM1-LSM7 COMPLEX, ASSOCIATION OF THE LSM1-LSM7 COMPLEX WITH PAT1 AND XRN1, FUNCTION OF THE LSM1-LSM7 COMPLEX, IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION OF THE LSM2-LSM8 COMPLEX WITH U6 SNRNA, IDENTIFICATION BY MASS SPECTROMETRY.
[8]"Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p."
Kufel J., Allmang C., Verdone L., Beggs J.D., Tollervey D.
Mol. Cell. Biol. 22:5248-5256(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PROCESSING OF PRE-TRNAS.
[9]"Lsm Proteins are required for normal processing and stability of ribosomal RNAs."
Kufel J., Allmang C., Petfalski E., Beggs J.D., Tollervey D.
J. Biol. Chem. 278:2147-2156(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PROCESSING OF PRE-RRNAS.
[10]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]"A complex pathway for 3' processing of the yeast U3 snoRNA."
Kufel J., Allmang C., Verdone L., Beggs J., Tollervey D.
Nucleic Acids Res. 31:6788-6797(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PROCESSING OF U3 SNORNA.
[12]"Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex."
Kufel J., Bousquet-Antonelli C., Beggs J.D., Tollervey D.
Mol. Cell. Biol. 24:9646-9657(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE LSM2-LSM8 COMPLEX IN NUCLEAR MRNA DEGRADATION.
[13]"Architecture of the Lsm1-7-Pat1 complex: a conserved assembly in eukaryotic mRNA turnover."
Sharif H., Conti E.
Cell Rep. 5:283-291(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 27-172 OF LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
[14]"Crystal structure and biochemical analysis of the heptameric Lsm1-7 complex."
Zhou L., Zhou Y., Hang J., Wan R., Lu G., Yan C., Shi Y.
Cell Res. 24:497-500(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF LSM1-LSM7 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-63.
[15]"Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation."
Wu D., Muhlrad D., Bowler M.W., Jiang S., Liu Z., Parker R., Song H.
Cell Res. 24:233-246(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.15 ANGSTROMS), SUBUNIT, INTERACTION WITH PAT1, FUNCTION, RNA-BINDING.
[16]"Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA."
Zhou L., Hang J., Zhou Y., Wan R., Lu G., Yin P., Yan C., Shi Y.
Nature 506:116-120(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF PHE-35; ASN-37 AND ARG-63.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X77291 Genomic DNA. Translation: CAA54505.1.
Z35787 Genomic DNA. Translation: CAA84845.1.
BK006936 Genomic DNA. Translation: DAA07094.1.
PIRS45760.
RefSeqNP_009527.1. NM_001178266.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70B2-95[»]
4C92X-ray2.30B2-95[»]
4M75X-ray2.95B/I1-95[»]
4M77X-ray3.11B/I1-95[»]
4M78X-ray2.79B/I1-95[»]
4M7AX-ray2.78B/I1-95[»]
4M7DX-ray2.60B/I1-95[»]
4N0AX-ray3.15C/D/G1-95[»]
ProteinModelPortalP38203.
SMRP38203. Positions 2-95.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32672. 92 interactions.
DIPDIP-794N.
IntActP38203. 65 interactions.
MINTMINT-383549.
STRING4932.YBL026W.

Proteomic databases

MaxQBP38203.
PaxDbP38203.
PeptideAtlasP38203.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYBL026W; YBL026W; YBL026W.
GeneID852255.
KEGGsce:YBL026W.

Organism-specific databases

CYGDYBL026w.
SGDS000000122. LSM2.

Phylogenomic databases

eggNOGCOG1958.
GeneTreeENSGT00390000016597.
HOGENOMHOG000166937.
KOK12621.
OMAKLDNISC.
OrthoDBEOG7PZSB0.

Enzyme and pathway databases

BioCycYEAST:G3O-28929-MONOMER.

Gene expression databases

GenevestigatorP38203.

Family and domain databases

InterProIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR016654. U6_snRNA_Lsm2.
[Graphical view]
PANTHERPTHR13829. PTHR13829. 1 hit.
PfamPF01423. LSM. 1 hit.
[Graphical view]
PIRSFPIRSF016394. U6_snRNA_Lsm2. 1 hit.
SMARTSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMSSF50182. SSF50182. 1 hit.
ProtoNetSearch...

Other

NextBio970835.
PROP38203.

Entry information

Entry nameLSM2_YEAST
AccessionPrimary (citable) accession number: P38203
Secondary accession number(s): D6VPX4
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: June 11, 2014
This is version 124 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome II

Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references